Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999960773537      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs25210 (probable pathogenic)
  • known disease mutation at this position (HGMD CM990648)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648156C>AN/A show variant in all transcripts   IGV
HGNC symbol GALT
Ensembl transcript ID ENST00000378842
Genbank transcript ID NM_000155
UniProt peptide P07902
alteration type single base exchange
alteration region CDS
DNA changes c.552C>A
cDNA.594C>A
g.10027C>A
AA changes H184Q Score: 24 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 184
frameshift no
known variant Reference ID: rs111033717
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs25210 (probable pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990648)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990648)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990648)
regulatory features H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.3131
-0.5610.877
(flanking)5.211
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased10027wt: 0.5619 / mu: 0.5663 (marginal change - not scored)wt: ATGGGCTGTTCTAACCCCCACCCCCACTGCCAGGTAAGGGT
mu: ATGGGCTGTTCTAACCCCCAACCCCACTGCCAGGTAAGGGT		 ccac|CCCC
Acc decreased10038wt: 0.87 / mu: 0.71wt: TAACCCCCACCCCCACTGCCAGGTAAGGGTGTCAGGGGCTC
mu: TAACCCCCAACCCCACTGCCAGGTAAGGGTGTCAGGGGCTC		 gcca|GGTA
Donor gained100220.45mu: CTAACCCCCAACCCC AACC|ccca
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      184NKGAMMGCSNPHPHCQVWASSFLP
mutated  not conserved    184SNPQPHCQVWASSFL
Ptroglodytes  all identical  ENSPTRG00000020886  184SNPHPHCQVWASSFL
Mmulatta  all identical  ENSMMUG00000020789  184SNPHPHCQVWASSFL
Fcatus  all identical  ENSFCAG00000016304  184SNPHPHCQVWASSFL
Mmusculus  all identical  ENSMUSG00000036073  165NKGAMMGCSNPHPHCQVWASSFL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  169NKGAMMGCSNPHPHCQVWASDFL
Drerio  all identical  ENSDARG00000069543  169NKGAMMGCSNPHPHCQVWASNFL
Dmelanogaster  all identical  FBgn0263200  163NKGAAMGCSNPHPHCQIWSCSFL
Celegans  all identical  ZK1058.3  165NRGAVVGCSNMHPHGQLWASNYL
Xtropicalis  not conserved  ENSXETG00000013206  151SK---CPCLCP------WVANAPAFT
protein features
start (aa)end (aa)featuredetails 
184184METALZinc (Potential).lost
186186ACT_SITETele-UMP-histidine intermediate (By similarity).might get lost (downstream of altered splice site)
202202METALIron (Potential).might get lost (downstream of altered splice site)
258259CONFLICTRR -> VG (in Ref. 1; AAC83409).might get lost (downstream of altered splice site)
301301METALIron (Potential).might get lost (downstream of altered splice site)
319319METALIron (Potential).might get lost (downstream of altered splice site)
321321METALIron (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1140 / 1140
position (AA) of stopcodon in wt / mu AA sequence 380 / 380
position of stopcodon in wt / mu cDNA 1182 / 1182
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 43 / 43
chromosome 9
strand 1
last intron/exon boundary 1102
theoretical NMD boundary in CDS 1009
length of CDS 1140
coding sequence (CDS) position 552
cDNA position
(for ins/del: last normal base / first normal base)		 594
gDNA position
(for ins/del: last normal base / first normal base)		 10027
chromosomal position
(for ins/del: last normal base / first normal base)		 34648156
original gDNA sequence snippet ATGGGCTGTTCTAACCCCCACCCCCACTGCCAGGTAAGGGT
altered gDNA sequence snippet ATGGGCTGTTCTAACCCCCAACCCCACTGCCAGGTAAGGGT
original cDNA sequence snippet ATGGGCTGTTCTAACCCCCACCCCCACTGCCAGGTATGGGC
altered cDNA sequence snippet ATGGGCTGTTCTAACCCCCAACCCCACTGCCAGGTATGGGC
wildtype AA sequence MSRSGTDPQQ RQQASEADAA AATFRANDHQ HIRYNPLQDE WVLVSAHRMK RPWQGQVEPQ
LLKTVPRHDP LNPLCPGAIR ANGEVNPQYD STFLFDNDFP ALQPDAPSPG PSDHPLFQAK
SARGVCKVMC FHPWSDVTLP LMSVPEIRAV VDAWASVTEE LGAQYPWVQI FENKGAMMGC
SNPHPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
mutated AA sequence MSRSGTDPQQ RQQASEADAA AATFRANDHQ HIRYNPLQDE WVLVSAHRMK RPWQGQVEPQ
LLKTVPRHDP LNPLCPGAIR ANGEVNPQYD STFLFDNDFP ALQPDAPSPG PSDHPLFQAK
SARGVCKVMC FHPWSDVTLP LMSVPEIRAV VDAWASVTEE LGAQYPWVQI FENKGAMMGC
SNPQPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 0.44 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project